GENE STRUCTURE PREDICTION USING INFORMATION ON HOMOLOGOUS PROTEIN-SEQUENCE

In this paper a new approach for the prediction of protein coding gene structures is described. The principal scheme of prediction is as fol lows: first, the exons with the best potential are predicted in a sequ ence with unknown functions and a list of potential amino acid fragmen ts coded by these exons is formed. Second testing the homology between each amino acid fragment from the list and proteins from the SWISS-PR OT database of amino acid sequences. One protein with the best homolog y is chosen out of all the homologous sequences. Third, reconstruction of the exon-intron structure, basing if on its homology, with the cho sen protein sequences. The method was tested on art independent contro l set (20 genes). The results were as follows: 21% of real exons were lost and 3% of non-real exons were found. This system can be used to r efine the results of gene prediction systems, especially if highly hom ologous proteins are found in the amino acid sequence database.